Aims of the AMBiCon project
Making biological phenomena predictable and to simulate entire cellular systems in the computer would be beneficial for biotechnological production of medication and personalized medicine. The genome-scale development of holistic, detailed, and reliable computer models incorporating physico-chemical constraints can only be feasible by using precise automated methods. This project aims to extend approaches for model creation. The effectiveness of the method are being experimentally validated on large-scale metabolic data. To this end, the project "automated multi-level modeling of biological systems considering physico-chemical constraints" (AMBiCon) has been established as an international collaboration project between the University of California, San Diego, and the University of Tuebingen, Tübingen, Germany.
Overview about this project
Watch these clips to learn more about the AMBiCon project:
See these and further clips also at the Systems-Biology YouTube channel.
About the schloar
For more information about the fellow, Dr. Andreas Dräger, see
- Gold medal for software development in team UC San Diego
- Outstanding presentation award by the F1000 journal at the BioVis Special Interest Group (SIG) meeting at ISMB in Orlando, FL, USA, July 2016
- Press release from August 11th 2015: Minimalausstattung für den Mikroorganismus
- Press release from August 10th 2015: Bioengineers identify the key genes and functions for sustaining microbial life
- Bin Du, Daniel Zielinski, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla Ruggiero, Garry Arzumanyan, and Bernhard O. Palsson. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Systems Biology, 10(1):1-15, June 2016. [ DOI | link ]
- Michael Römer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, and Andreas Zell. ZBIT Bioinformatics Toolbox: a Web-Platform for Systems Biology and Expression Data Analysis. PLoS ONE, February 2016. [ DOI ]
- Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, and Ulrich M. Zanger. Coordinating role of RXRα in downregulating hepatic detoxification during inflammation revealed by fuzzy-logic modeling. PLoS Computational Biology, January 2016. [ DOI ]
- Zachary A. King, Justin S. Lu, Andreas Dräger, Philip C. Miller, Stephen Federowicz, Joshua A Lerman, Ali Ebrahim, Bernhard O. Palsson, and Nathan E. Lewis. BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucleic Acids Research, October 2015. [ DOI | link | pdf ]
- Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P. Burgard, Roger L. Chang, Andreas Dräger, Iman Famili, Adam M. Feist, Ronan M. T. Fleming, Stephen S. Fong, Vassily Hatzimanikatis, Markus J. Herrgard, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A. Lerman, Nathan E. Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Jennifer L. Reed, Michael Saunders, Ryan S. Senger, Nikolaus Sonnenschein, Yuekai Sun, and Ines Thiele. Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11(10), October 2015. [ DOI | link | pdf ]
- Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, and Bernhard O. Palsson. SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks. BMC Systems Biology, 9(1):1-17, September 2015. [ DOI | link | PDF ]
- Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, and Darren J. Wilkinson. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics, 12(2):271, September 2015. [ DOI | link | PDF ]
- Laurence Yang, Justin Tan, Edward J. O'Brien, Jonathan Monk, Donghyuk Kim, Howard J. Lia, Pep Charusantia, Ali Ebrahim, Colton J. Lloyd, James T. Yurkovich, Bin Du, Andreas Dräger, Alex Thomas, Yuekai Sun, Michael A. Saunders, and Bernhard O. Palsson. A systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences, August 2015. [ DOI | PDF | link ]
- Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard Ø. Palsson. Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Computational Biology, 11(8):e1004321, August 2015 [ DOI | link ].
- Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, and Andreas Dräger. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics, June 2015 [DOI | link ].
- Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computational Biology, December 2014. [DOI | link | PDF ]
- Andreas Dräger and Bernhard Ø. Palsson. Improving collaboration by standardization efforts in systems biology. Frontiers in Bioengineering, 2(61), December 2014. [ DOI | link ]
- Claudine Chaouiya, Duncan Berenguier, Sarah M. Keating, Aurelien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Dennis Thierffry, Nicolas Le Novère, Julio Saez-Rodriguez, and Tomáš Helikar. SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology, 7(1):135, December 2013. [ DOI | link | pdf ]
- Johannes Eichner, Florian Topf, Andreas Dräger, Clemens Wrzodek, Dierk Wanke, and Andreas Zell. TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors. PLoS ONE, 8(12):e82238, December 2013. [ DOI | link | pdf ]
- Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, and Nicolas Le Novère. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7(1):116, November 2013. [ DOI | link | PDF ]
- Finja Büchel, Sandra Saliger, Andreas Dräger, Stephanie Hoffmann, Clemens Wrzodek, Andreas Zell, and Philipp J. Kahle. Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. BMC Neuroscience, 14(136), November 2013. [ DOI | link | pdf ]
- Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger. The systems biology simulation core algorithm. BMC Systems Biology, 7:55, July 2013. [ DOI | link | pdf ]
- Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Metabolic Networks, pages 1249-1251. Springer-Verlag, New York, August 2013. [ DOI | link ]
- Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Parameter Estimation, Metabolic Network Modeling, pages 1627-1631. Springer-Verlag, New York, August 2013. [ DOI | link ]
To try many of the tools listed below online without installation, visit the web-service facility at the Center for Bioinformatics Tuebingen: https://webservices.cs.uni-tuebingen.de.
- 10/10/2016 EscherConverter version 1.1
- 08/21/2016 EscherConverter version 1.0
- 07/02/2016 ModelPolisher version 1.4
- 06/21/2016 EscherConverter version 0.5
- 04/30/2016 ModelPolisher version 1.3
- 03/05/2016 ModelPolisher version 1.2
- 01/24/2016 ModelPolisher version 1.1
- 10/19/2015 ModelPolisher version 1.0
- 09/17/2015 KEGGtranslator version 2.5 in collaboration with University of Tuebingen
- 08/10/2015 SBMLsqueezer version 2.1 in collaboration with University of Tuebingen
- 06/12/2015 JSBML version 1.1
- 02/06/2015 KEGGtranslator version 2.4 in collaboration with University of Tuebingen
- 12/09/2014 JSBML version 1.0 in collaboration with Caltech and EBI
- 10/24/2014 SBMLsqueezer version 2.0.1 in collaboration with University of Tuebingen
- 09/24/2014: JSBML version 1.0rc1 in collaboration with Caltech and EBI
- 03/06/2014: JSBML version 1.0β1 in collaboration with Caltech and EBI
- 03/17/2014: Systems Biology Simulation Core Library version 1.4 (SBSCL) in collaboration with EBI and University of Tuebingen
- 07/17/2014: SBMLsimulator version 1.2.1 in collaboration with University of Tuebingen
- 06/30/2014 SBMLsqueezer version 2.0 in collaboration with University of Tuebingen
- Winter semester 2014: Systems biology: Simulation of Dynamic Network States, Lecture with excercises, 2+2 SWS, Mondays 4-6 p.m. and Tutorial on Tuesdays 2-4 p.m.
- Summer semester 2016: Software engineering practical class at the University of Tuebingen
- Contribution to the class BENG 123 (Bioengineering)
Student mentoring programs
- Google Summer of Code 2014
- International Genetically Engineered Machine (iGEM) Competition 2014
- National Resource for Network Biology (NRNB) Summer of Code 2015
- Google Summer of Code 2016
- International Genetically Engineered Machine (iGEM) Competition 2016
Conference presentations and international meetings
- Meeting with Biosustainability group of the Technical University of Denmark in Copenhagen, DK, September 10 to September 13 2013
- Conference talk at COMBINE 2013 in Paris, France, at September 16th to September 20th 2013. See the meeting report for details.
- Participation in the 13th Annual Conference of the German Academic International Network in San Francisco, CA, USA, August 30 to September 1 2013
- Meeting with Dr. Hucka at Caltech, Pasadena, CA at October 15 2013
- Participation in the European Talent Fair in Boston, MA, USA, January 31 to February 2 2014.
- Remote participation in HARMONY workshop in Manchester, UK, in April 2014
- COBRA modeling conference in Charlottesville, VA, USA in May 2014
- Chaired session at COMBINE 2014 about the results of the Google Summer of Code 2014 project for the development of JSBML in Los Angeles, August 20th 2014. See the meeting's agenda for details.
- 14th Annual Conference of the German Academic Network in Boston, MA, (September 5 to September 7 2014)
- Poster presentation entitled "New Standard Resources for Systems Biology: BiGG Models Database and the Visual Pathway Editor Escher" COBRA modeling conference in Heidelberg, Germany, September 2015
- Presentation on "New Standard Resources for Systems Biology: BiGG 2 Database and Visual Pathway Editing with Escher" during the COMBINE 2015 in Salt Lake City, UT, USA, October 2015.
- 6th International Conference on Systems Biology of Mammalian Cells (SBMC) in Munich, Germany, April 2016.
- Conference co-organization and session chaired session during 1st SysMod SIG (Special Interest Group) meeting at ISMB on "Modeling metabolism: from kinetics to whole genome" and presentation about "The ZBIT systems biology software and web service collection" during 1st SysMod SIG in Orlando, FL, USA 2016
- Outstanding presentation award sponsored by the F1000 journal for the poster "New Standard Resources for Systems Biology: BiGG Models Database and the Visual Pathway Editor Escher" at BioVis in Orlando, FL
- Presentation on constraint-based modeling and reconstruction of biological networks during the bioinformatics summer school at the Swiss Institute of Bioinformatics (SIB) in Lausanne, Switzerland, in August 2016.
The project AMBiCon is funded by the 7th EU Framework Program for Research and Technological Development in form of a Marie-Curie International Outgoing Fellowship (IOF) awarded to Andreas Dräger (grant number 332020).